Using the node editor in a private project
While it isn't documented much, blender does support custom node trees. You can start with the custom nodetree template in blenders text editor. You may also find some help searching here for pynode.

Two example projects using custom node trees are animation nodes and sverchok.

As you are defining each nodes functionality, you don't have to access or modify blenders data, so you could use blenders node editor while making each node read/write data to files.